BIOLOGICAL DIVERSITY:
CLASSIFICATION

Table of Contents

Biological
Diversity and Classification

Taxonomy
is that branch of biology dealing with the identification and naming
of organisms. The ancient Greek philosopher Aristotle apparently
began the discussion on taxonomy. British naturalist John Ray is
credited with revising the concept of naming and describing
organisms. During the 1700s, Swedish botanist Carolus Linneus
classified all then-known organisms into two large groups: the
kingdoms Plantae and Animalia. Robert Whittaker in 1969 proposed five
kingdoms: Plantae, Animalia, Fungi, Protista, and Monera. Other
schemes involving an even greater number of kingdoms have lately been
proposed, however most biologists employ Whittaker's five kingdoms.
Recent studies suggest that three domains be employed: Archaea,
Bacteria, and Eukarya. The classification of a rose is shown in
Figure 1, while that of a warbler is illustrated in Figure 2.

Figure 1. Taxonomy of a selected plant
species. Note the increasing inclusivity of the "higher"
taxonomic ranks. Kingdoms have a great deal more types of
creatures in them than do species. Image from Purves et al.,
Life: The Science of Biology, 4th Edition, by Sinauer
Associates (www.sinauer.com)
and WH Freeman (www.whfreeman.com),
used with permission.

Figure 2.Classification of a single species of
animal. Note the similar composition of the animal kngdom
above as compared to the plant kingdom.Image from Purves et al., Life: The
Science of Biology, 4th Edition, by Sinauer Associates
(www.sinauer.com)
and WH Freeman (www.whfreeman.com),
used with permission.

Linneus
attempted to pigeon-hole (or classify) all known species of his time
(1753). Linnean hierarchical classification was based on the premise
that the species
was the smallest unit, and that each species (or taxon)
nested within a higher category.

Linneus also developed the concept of
binomial
nomenclature, whereby scientists speaking
and writing different languages could communicate clearly. For
example Man in English is Hombre in Spanish, Herr in
German, Ren in Chinese, and Homo in Latin. Linneus
settled on Latin, which was the language of learned men at that time.
If a scientist refers today to Homo, all scientists know what
organism/taxon he or she means.

Taxonomy
is part of a larger division of biology known as systematics.
Determination of phylogeny
is a goal of systematics. This is done by the construction of
phylogenetic trees, which in a sense represent evolutionary
hypotheses and attempts to define monophyletic
groups. To build these trees, we must have
data, which comes from the characteristics used in classification.
There are several methods of classification: traditional, phentic,
and cladistic. They differ in how they value certain characters.
Let's consider how traditional classification treats reptiles, birds,
and mammals, as shown in Figure 3.

Traditional Classification

Data used in traditional systematics stresses both
common ancestry (monophylesis) and the amount of divergence among
groups. The traditional, dating to Linneaus view, is that birds have
feathers, reptiles have scales, and mammals have hair. Using this as
a major character, a classification like that above has been
constructed. Fossils,
evidence of past life, are not included in this classification. Since
all of these groups have the amniotic
egg, or a modification of it, they would
be united in a larger taxon. Linneus placed each of these groups in a
separate class within the Phylum Chordata. A primitive character is
one present in the common ancestor and all members of the group, such
as the amniotic egg. A derived character is one found only in a
particular lineage within the larger group. In our example above,
hair and feathers may be viewed as derived characters. A traditional
view of our example group is that birds and mammals evolved from
reptiles due to their unique derived characters.

Cladistics and Cladograms

Cladistics is a type of systematics developed by
the late German biologist Willi Hennig, who attempted to formulate a
more objective method of classifying organisms. Cladists group
organisms based on the presence of shared derived characters, not the
overall similarity of potential group members. In the example cited
in Figure 3, the amniotic egg would be used to unite a group sharing
common ancestry, since it would NOT be present in a group that was
not in the lineage. The use of feathers and hair to separate birds
and mammals from reptiles would NOT factor into a cladistic
hypothesis, or cladogram, since these are characters unique to only
one taxon in our group. Such an approach is shown in Figure 4.

The value of cladistics lies in its capacity to
generate (and provide a set of criteria for the evaluation) of
multiple hypotheses (alternate cladograms) that can be evaluated with
additional data. Almost always the "correct" cladogram employs the
principle of parsimony, which proposes that the shortest number of
steps or character state changes is most likely correct. An important
question....is evolution always parsimonmious? However the ultimate
answer to that question unfolds, the rigor cladistics introduces to
systematics is useful in getting traditional systematists to look at
their subjective classifications in a new light. On the diagram shown
in Figure 5, shared derived characters are indicated as hauchers
across the lines. The mammal clade (in this case represented by mouse
and chimpanzee) is united by fur, the lizard, pigeon, mouse-chimp
clade is united by claws or nails, etc.

Figure 5. Cladogram of the vertebrate
chordates.Image from Purves et al.,
Life: The Science of Biology, 4th Edition, by Sinauer
Associates (www.sinauer.com)
and WH Freeman (www.whfreeman.com),
used with permission.

Cladistic Classification

The example used above, if treated cladistically,
would produce a very different classification! Note that crocodiles
have more in common (in a cladistic sense) with birds than they do
with other reptiles. Birds and crocs form a clade, or monophyletic
group united by shared derived characters not present in the other
groups. If we construct a Linnean group from this cladogram, we have
a class of birds and crocodiles, a second class of lizards, snakes,
and turtles, and a third class of mammals, as shown in Figure 6.

Figure 6. Cladistic-based classification
of reptiles, birds, and mammals. Note the changes betweeen
the cladistic and traditional classifications as shown in
Figure 3.Image from Purves et al.,
Life: The Science of Biology, 4th Edition, by Sinauer
Associates (www.sinauer.com)
and WH Freeman (www.whfreeman.com),
used with permission.

One of the more interesting applications of
cladistics is to the question of the pandas. The giant panda was once
thought to be a bear, but later its racoon-like characters caused it
to be placed closer to racoons. The red (lesser) panda lives in the
same areas of China as the giant panda, but has a far greater
similarity with racoons, as shown in Figure 7. DNA hybridization
studies suggest the giant panda is in the bear clade, while the red
panda is in the racoon clade. Both share a common ancestry, as
indicated by shared derived characters, followed by convergent
evolution of other characters. The diagram above indicates this
divergence from common ancestry, and even attempts to show the time
of that divergence.

Figure 7. Cladistic analysis of the
relationships of the giant and lesser pands. Note: time has
been added onthe horizontal scale after the cladistic
analysis was done.Image from Purves
et al., Life: The Science of Biology, 4th Edition, by
Sinauer Associates (www.sinauer.com)
and WH Freeman (www.whfreeman.com),
used with permission.

Phenetics

Phenetics is a process by which taxa are clustered
together based on the number of their similarities (or differences,
depending on the numerical coefficient employed). Traits are measured
and either converted into integers or input directly as numerical
data. Theses data are then mathematically processed using an
algorithm that generates a similarity (or distance as the case may
be) matrix. Various graphical representations of this matrix include
a phenogram, and principal coordinate plot. Phenetic classifications
are plagued by problems of convergence and parallelism, but are
useful in their attempt to objectify the classification process. My
previous work on triprojectate pollen employed phenetics to deal with
a wide array of subjective ratios or other classification methods.
Convergence was a given with this group of fossil pollen produced by
one or more groups of unknown extinct plants. Since monophylesis
could not be established for the entire group, phenetics was use to
help delineate possible monophyletic groups for eventual cladistic
study.

The naming of species and other taxa follows a set
of rules, the International Code of Botanical Nomenclature (ICBN,
click here
for an online version) for plants, the International Code of
Zoological Nomenclature (ICZN) for animals.

Some general rules for nomenclature:

All taxa must belong to a higher taxonomic
group. Often a newly discovered organism is the sole species in a
single genus, within a single family...etc.

The first name to be validly and effectively
published has priority. This rule has caused numerous name
changes, especially with fossil organisms: Brontosaurus is
invalid, and the correct name for the big sauropod dinosaur is
Apatosaurus, Eohippus (the tiny "dawn horse") is
invalid and should be referred to as Hyracotherium.
Sometime, however, names can be conserved if a group of
systematists agrees.

All taxa must have an author. When you see a
scientific name such as Homo sapiens L, the L stands for
Linneus, who first described and named that organism. Most
scientists must have their names spelled out, for example
Libopollis jarzenii Farabee et al. (an interesting fossil
pollen type I stumbled across a very long time ago!).

Linnaeus originally placed all living things into
either the plant or animal kingdoms. As scientists learned more about
the biology of many organisms, this constraining into two kingdoms
became less and less defensible.

Evolutionary theory and the cell theory provide us
with a basis for the interrelation of all living things. We also
utilize Linneus' hierarchical classification system, adopting
(generally) five kingdoms of living organisms. Viruses,
as discussed later, are not considered living. Recent studies suggest
that there might be a sixth Kingdom, the Archaea.

Monera are the only kingdom composed of
prokaryotic organisms, they have a cell wall, and lack both
membrane-bound organelles and multicellular forms. The
Archaebacteria, the most ancient of this kingdom, are so different
that they may belong to a separate kingdom. Other groups of Monera
include the cyanobacteria (autotrophic) and eubacteria
(heterotrophic).

Protista

The most ancient eukaryotic kingdom, protists
include a variety of eukaryotic body
(single-celled-colonial-multicellular?) and nutritional
heterotrophic, autotrophic, and both) forms. Perhaps they are best
defined as eukaryotes that are NOT fungi, animals, or plants.

Fungi

Fungi are a eukaryotic, heterotrophic, usually
multicellular group having multinucleated cells enclosed in cells
with cell walls. They obtain their energy by decomposing dead and
dying organisms and absorbing their nutrients from those organisms.
Some fungi also cause disease (yeast infections, rusts, and smuts),
while others are useful in baking, brewing, as foods, drugs and
sources for antibiotics.

Plantae

Plants are immobile, multicellular eukaryotes that
produce their food by photosynthesis and have cells encased in
cellulose cell walls. Plants are important sources of oxygen, food,
and clothing/construction materials, as well as pigments, spices,
dyes, and drugs.

Animalia

Animals are multicellular, heterotrophic
eukaryotes that are capable of mobility at some stage during their
lives, and that have cells lacking cell walls. Animals provide food,
clothing, fats, scents, companionship, and labor.